Bob,
Needless to say, I'm heavy into playing with this already. One problem
on my end: The minimize command by itself seems to be broken. This is on
a fresh page load prior to "set picking dragMinimize."
Harping on a Point: As chemists, the model kit was our first educational
touch of intimacy with molecules. It was one of the components of our
education that turned us on to chemistry - our own Maria Montessori
thing. I agree. This is a wonderful addition to Jmol.
Otis
On 5/21/2010 9:01 AM, Robert Hanson wrote:
First - I should point out that this required almost no coding -- we
already had minimization and bindings; this just added a couple of new
options and a bit of stitching. I'm not sure "set picking
dragMinimize" is quite the right way to do this, but it's OK for this
week.
Ah, yes, what to do with it??
My organic class and I were reviewing for the final last night. I
popped up methylcyclohexane and started quizzing them in relation to
gauche interactions and conformations. It was quite fun to just tug on
the molecule to switch from equatorial to axial or from chair to
twist-boat. I think the energies in UFF might be meaningless, but the
ease of manipulating the model this way was great fun and way faster
than anything else I've ever used -- no setup, no special page, just
pull in the molecule and start tugging.
It would have been especially nice to just be able to hover over an
atom or bond and delete it or modify it. I have a hunch that if you
added to this a simple model building kit (mostly just a few
context-sensitive drop-down menus that would appear when you hover
over an atom, I think), it would pretty much take care of anything I
would need in teaching about structure in relation to conformations of
cyclohexane -- except for a couple of pages like
http://chemapps.stolaf.edu/jmol/docs/examples-11/jmol-flot-energy.htm,
which is based on a more refined optimization. (Note that you can just
drag-and-drop a Spartan file from your hard drive in there, and it
will display its full energy profile.)
In addition, since now we can test for matches to specific
conformations, already it would be simple enough to write a
blank-slate page that would ask the student questions like, "Shown
below is 2-methylcyclohexane. By pulling on atoms, change this model
to one that is a chair conformation that has an axial methyl group."
-- and then test for that using the COMPARE function. I think it opens
up some interesting possibilities that we haven't had before.
I was thinking before that it has "questionable pedagogic value"
because obviously you can't really do this sort of thing with a
molecule, but as I think about it more, you can't just click on an
atom in a real molecule and invert stereochemistry at that center,
either! So every "model kit" has its deceit.
One wonders, though, to a certain extent, does a molecule "respond" to
at least minor distortions this way? I was intrigued by how the whole
molecule responded when I yanked hard on an H atom. I honestly had
never thought of that before, and only had thought of interactions
such as that as being far more localized. But as I play with it and
think about the forces involved, I have to say I think there's
something there.
Still pondering this.
Bob
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Otis Rothenberger
chemagic.com
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